Graft-versus-host disease is a serious complication following hematopoietic stem cell transplantation (HSCT), with a high mortality rate. A clearer understanding of the molecular pathogenesis may allow robust biomarker identification and improved therapeutic options. MicroRNAs (miRNAs) are short non-coding regulatory RNAs that are expressed in both tissue and body fluids, and show great potential as clinically translatable biomarkers. Here we discuss the field of miRNA biomarker discovery in the setting of HSCT.

by Dr Rachel E. Crossland and Prof. Anne M. Dickinson

Allogeneic hematopoietic stem cell transplant and graft-versus-host disease
Allogeneic hematopoietic stem cell transplant (allo-HSCT) is a curative treatment for many blood cancers. It is based on the transplant of hematopoietic blood and marrow stem cells from related or unrelated donors, and over 17 000 allo-HSCT transplants a year are carried out in Europe. The therapy is curative due to the properties of subsets of donor-derived lymphocytes, including T-cells and natural killer cells, that are able to eradicate residual malignancy due to their ‘graft-versus-leukemia’ (GvL) effects. However, T-cells can also give rise to a life-threatening complication, called graft-versus-host disease (GvHD).

GvHD affects 40–70 % of HSCT patients, and severe disease is associated with 40–60 % mortality. The pathology of GvHD is not completely understood, but has been generally attributed to three main stages:

1. Initiation by tissue damage, due to transplant conditioning regimens, that in turn activate the host antigen-presenting cells (APCs).
2. Activation of donor T-cells by APCs, also known as the afferent phase.
3. Finally, in efferent phase, cellular and inflammatory factors work together to damage the target organs. GvHD is the most important and potentially fatal complication of HSCT and can present in both acute and chronic forms.

Acute GvHD (aGvHD) typically occurs within the first 100 days following transplantation and primarily presents in the skin, liver and gastrointestinal tract as an erythematous maculopapular rash, elevated bilirubin, and diarrhoea and vomiting, respectively [1]. Chronic GvHD (cGvHD) has a more delayed onset, and is a multi-organ allo- and auto-immune disorder that most frequently affects the skin, lung, mouth, liver, eye, joints and gastrointestinal tract causing a plethora of co-morbidities including cardiovascular, gastrointestinal, hepatic, pulmonary, endocrine, bone and joint disorders, infections and secondary malignancies. GvHD is commonly treated with immunosuppressants, which increase the patient’s susceptibility to life-threatening infections. Therefore, survival rates after allo-HSCT have not improved for over two decades, owing to major complications such as infections, GvHD and relapse of malignant disease. To date, GvHD can be well characterized by established and clinically validated GvHD grading scales and measurements of the National Institute of Health (NIH) Consensus classification. However, there is a lack of understanding of the immunobiology and metabolic triggers that cause the development and further perpetuation of GvHD, especially cGvHD and subsequent co-morbidity.

GvHD and biomarkers
Biomarkers are being increasingly used in the prediction, prognosis and diagnosis of diseases and are now being validated for prediction of outcome in patients with GvHD. Predicting and preventing GvHD would allow clinicians to develop of risk-adapted clinical protocols, encourage a curative GvL response and improve outcomes, including transplant survival rates and long-term complications. However, despite the frequency and significance of GvHD, there are currently no early diagnostic or predictive markers that have been validated for use in clinic. This may be attributed to a lack of understanding of the molecular pathobiology of aGvHD on a systemic level. Determining the molecular pathways involved at initiation of aGvHD will identify novel targets for therapeutic intervention, and these factors may have the potential to act as biomarkers for aGvHD.

MicroRNAs as biomarkers
MicroRNAs (miRNAs) represent a promising source of biomarkers for GvHD because they play critical roles in the development and function of the immune system and in transplant biology (Fig. 1). MiRNAs represent a family of small (19–24 nucleotide) non-coding RNAs, which affect the regulation of gene expression in eukaryotic cells by binding to the 3´-untranslated region of target messenger RNAs [2]. They are predicted to target around 50 % of all genes and play an important role in fundamental cellular processes such as development, stem cell division, apoptosis and cancer. MiRNAs represent ideal candidates for biomarker identification in GvHD as they can be assessed using accurate and sensitive technology (e.g. NanoString/qRT-PCR), quantified in bodily fluids that require minimally invasive sample collection (e.g. serum/urine) and further investigated for biological function (e.g. target protein identification) that may expand upon our understanding of GvHD pathology. Although the field of GvHD-related miRNA research is in its infancy, recent studies have demonstrated an emerging role for miRNAs as GvHD biomarkers.

MiRNAs as biomarkers for GvHD
MiR-155 was one of the first miRNAs to be associated with the regulation of aGvHD. This miRNA is a critical regulator of inflammation, as well as adaptive and innate immune responses. In 2012, Ranganathan et al. demonstrated upregulation of miR-155 in the T-cells of mice and patients developing aGvHD following HSCT [3]. Serum expression levels also correlated with GvHD severity, and serum IFN-gamma, IL-17 and IL-9 levels, suggesting the potential of miR-155 as a biomarker for aGvHD diagnosis, and as a therapeutic target. It has since been demonstrated that miR-155 expression in both donor CD8+ T-cells and conventional CD4+ CD25− T-cells is pivotal for aGvHD pathogenesis, and drives a pro-inflammatory Th1 phenotype in donor T-cells [4].

MiR-146 is increasingly being recognized as a ‘fine-tuner’ of cell function and differentiation in both innate and the adaptive immunity. MiR-146a controls innate immune cell and T-cell responses, and directly targets two adapter proteins in the nuclear factor-kappa B (NF-κB) activation pathway; tumour necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and IL-1 receptor-associated kinase 1 (IRAK1) [5]. In addition, the survival and maturation of human plasmacytoid dendritic cells that are involved in GvHD can be regulated by miR-146a. With regard to GvHD, miR-146a has been shown to be upregulated in the T-cells of nice developing aGvHD, and transplanting miR-146a–/– T-cells causes increased GvHD severity, elevated TNF serum levels and reduced survival [6]. Interestingly, Stickel et al. observed downregulation of miR-146a shortly following allo-HCT in mice (day 2), followed by upregulation in T-cells later in the aGvHD reaction (days 6 and 12), which they hypothesized may be a rescue mechanism to counteract inflammation [6]. Expression of miR-146a has since been identified to show a statistical interaction with expression of miR-155 in the peripheral blood of allo-HSCT patients before disease onset, and this interaction was predictive of aGvHD incidence, further implicating its potential as a GvHD biomarker [7].

Serum expression of miR-29a has recently been implicated as a potential biomarker for GvHD. Ranganathan et al. showed in two independent cohorts that miR-29a is significantly upregulated in allo-HSCT patients at aGvHD onset compared with non-aGvHD patients, and as early as 2 weeks before symptomatic disease onset compared to time-matched controls [8]. Further investigation into the function of miR-29a showed that it binds to and activates dendritic cells, via toll-like receptor (TLR)7 and TLR8, resulting in the activation of the NF-κB pathway and secretion of pro-inflammatory cytokines. Treatment with locked nucleic acid anti-miR-29a significantly improved survival in a mouse model of aGvHD, while retaining GvL effects [8].

In 2013 an elegant study by Xiao et al. investigated miRNA expression profiles in the plasma of patients with aGvHD, compared to patients with no aGvHD, using a qRT-PCR array to include 345 miRNAs [9]. The study identified a final signature of four miRNAs (miR-423, miR-199-3p, miR-93*, and miR-377) that significantly predicted for aGvHD at 6 weeks post-HSCT, before the onset of symptoms. Furthermore, the model was associated with disease severity and poor overall survivall [9]. Gimondi et al. have also profiled circulating miRNA expression using a qRT-PCR platform, based on samples collected 28 days post-HSCT [10]. They detected 27 miRNAs that could collectively discriminate between aGvHD and non-aGvHD. MiR-194 and miR-518f were significantly upregulated in patients who later developed aGvHD, and these miRNAs were predicted to target critical pathways implicated in aGvHD pathogenesis [10]. Our laboratory has used NanoString technology to comprehensively profile the expression of n=799 mature miRNAs in the serum of patients who had undergone HSCT, to identify miRNAs with altered expression at aGvHD diagnosis (Fig. 2) [11]. Assessment of selected miRNAs was also replicated in independent cohorts of serum samples taken at aGvHD diagnosis and before disease onset to assess their prognostic potential. Expression analysis identified 61 miRNAs that were differentially expressed at aGvHD diagnosis, and miR-146a, miR-30b-5p, miR-374-5p, miR-181a, miR-20a, and miR-15a were significantly verified in an independent cohort. MiR-146a, miR-20a, miR-18, miR-19a, miR-19b, and miR-451 were also differentially expressed 14 days post-HSCT, before the onset of symptoms, in patients who later developed aGvHD. High miR-19b expression was associated with improved overall survival, whereas high miR-20a and miR-30b-5p were associated with lower rates of non-relapse mortality and improved overall survival [11]. Collectively, these miRNA profiling studies highlight that circulating biofluid miRNAs show altered expression at aGvHD onset and have the capacity to act as independent markers for prediction, prognosis and diagnosis of GvHD.

Future directions
Despite greater recognition of the potential for miRNAs as clinically adaptable biomarkers, they have not yet reached translation to the clinic. This is predominantly because of the lack of reproducibility and independent validation to date. Indeed, owing to the high degree of variability in factors when designing and performing miRNA profiling experiments, which may be attributed to clinical (patient characteristics, sampling time points and type of body fluid analysed), technical (sample preparation, miRNA profiling platform and spectrum of miRNAs profiled) and analytical (normalization strategy) factors, progress has been slow in realizing their full potential. Despite contradictory research results on the biological basis of GvHD, low patient cohorts in single transplant centre studies, insufficient characterization of GvHD and lack of understanding and knowledge of GvHD’s impact on the immune system, miRNA biomarkers continue to show promise, but many studies are still in their infancy. Future progress relies on collaboration between research groups, focusing on standardization of the samples, protocols and technologies used, which will greatly improve the reproducibility of findings allowing for extended validation of miRNAs of interest. The ultimate aim will be to diagnose GvHD and predict outcome before the onset of clinical symptoms, allowing for earlier therapy and personalized treatments and leading to reduced mortality and morbidity outcomes.
References
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The authors
Rachel E. Crossland* PhD and Anne M. Dickinson PhD
Haematological Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK

*Corresponding author
E-mail: Rachel.crossland@ncl.ac.uk
Twitter: @RECrossland

Genome-wide analysis of circulating cell-free DNA copy number detects active melanoma and predicts survival
Silva S, Danson S, Teare D, Taylor F, Bradford J, et al. Clin Chem 2018; 64(9): 1338–1346.

BACKGROUND: A substantial number of melanoma patients develop local or metastatic recurrence, and early detection of these is vital to maximize benefit from new therapies such as inhibitors of BRAF and MEK, or immune checkpoints. This study explored the use of novel DNA copy-number profiles in circulating cell-free DNA (cfDNA) as a potential biomarker of active disease and survival.

PATIENTS AND METHODS: Melanoma patients were recruited from oncology and dermatology clinics in Sheffield, UK, and cfDNA was isolated from stored blood plasma. Using low-coverage whole-genome sequencing, we created copy-number profiles from cfDNA from 83 melanoma patients, 44 of whom had active disease. We used scoring algorithms to summarize copy-number aberrations and investigated their utility in multivariable logistic and Cox regression analyses.

RESULTS: The copy-number aberration score (CNAS) was a good discriminator of active disease (odds ratio, 3.1; 95 % CI, 1.5–6.2; P=0.002), and CNAS above or below the 75th percentile remained a significant discriminator in multivariable analysis for active disease (P=0.019, with area under ROC curve of 0.90). Additionally, mortality was higher in those with CNASs above the 75th percentile than in those with lower scores (HR, 3.4; 95 % CI, 1.5–7.9; P=0.005), adjusting for stage of disease, disease status (active or resected), BRAF status, and cfDNA concentration.

CONCLUSIONS: This study demonstrates the potential of a de novo approach utilizing copy-number profiling of cfDNA as a biomarker of active disease and survival in melanoma. Longitudinal analysis of copy-number profiles as an early marker of relapsed disease is warranted.

Microbiological diagnostics of bloodstream infections in Europe – An ESGBIES survey
Idelevich EA, Seifert H, Sundqvist M, Scudeller L, Amit S, et al. Clin Microbiol Infect 2019; doi: 10.1016/j.cmi.2019.03.024 [Epub ahead of print].

OBJECTIVES: High-quality diagnosis of bloodstream infections (BSIs) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories.

METHODS: We performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries.

RESULTS: Responses were received from 209 laboratories in 25 European countries. While 32.5 % (68/209) of laboratories only used the classical processing of positive blood cultures (BCs), two-thirds applied rapid technologies. Of laboratories that provided data for respective question, 42.2 % (78/185) were able to start incubating blood cultures in automated BC incubators around-the-clock, and only 13 % (25/192) had established a 24-hour service to start immediate processing of positive BCs. Only 4.7 % (9/190) of laboratories validated and transmitted the results of identification and antimicrobial susceptibility testing (AST) of BC pathogens to clinicians 24 hours/day. MALDI-TOF MS from shortly incubated sub-cultures on solid media was the most commonly used approach to rapid pathogen identification from positive BCs, and direct disk diffusion was the most common rapid AST method from positive BCs.

CONCLUSIONS: Laboratories have started to implement novel technologies for rapid identification and AST for positive BCs. However, progress is severely compromised by limited operating hours such that current practice of BC diagnostics in Europe complies only partly with the requirements for optimal BSI management.

An integrated next-generation sequencing system for analyzing DNA mutations, gene fusions, and RNA expression in lung cancer
Haynes BC, Blidner RA, Cardwell RD, Zeigler R, Gokul S, et al. Transl Oncol 2019; 12(6): 836–845.

We developed and characterized a next-generation sequencing (NGS) technology for streamlined analysis of DNA and RNA using low-input, low-quality cancer specimens. A single-workflow, targeted NGS panel for non-small cell lung cancer (NSCLC) was designed covering 135 RNA and 55 DNA disease-relevant targets. This multiomic panel was used to assess 219 formalin-fixed paraffin-embedded NSCLC surgical resections and core needle biopsies. Mutations and expression phenotypes were identified consistent with previous large-scale genomic studies, including mutually exclusive DNA and RNA oncogenic driver events. Evaluation of a second cohort of low cell count fine-needle aspirate smears from the BATTLE-2 trial yielded 97 % agreement with an independent, validated NGS panel that was used with matched surgical specimens. Collectively, our data indicate that broad, clinically actionable insights that previously required independent assays, workflows, and analyses to assess both DNA and RNA can be conjoined in a first-tier, highly multiplexed NGS test, thereby providing faster, simpler, and more economical results.

Molecular diagnosis of asparagine synthetase (ASNS) deficiency in two Indian families and literature review of 29 ASNS deficient cases
Devi ARR, Naushad SM. Gene 2019; doi: 10.1016/j.gene.2019.04.024 [Epub ahead of print].

In the current study, we report three cases of asparagine synthetase (ASNS) deficiency from two consanguineous families. Family 1 had two early neonatal deaths due to a novel mutation in the ASNS gene c.788C > T (p.S263F) and both the children presented with microcephaly and one of them had severe intracranial hemorrhage. The proband from the second family was homozygous for c.146G > A (p.R49Q) and manifested myoclonic seizures, developmental delay, coarse hair and diffuse cortical atrophy. Molecular docking studies of both the mutations revealed alteration in the ligand binding site. To date, 26 mutations were reported in ASNS gene in 29 affected children indicating high degree of genetic heterogeneity and high mortality. Although asparagine depletion is not of diagnostic utility, multiple linear regression model suggested that asparagine levels vary to the extent of 20.6 % based on glutamine and aspartate levels and ASNS deficiency results in depletion of arginine synthesis. ASNS deficiency should be suspected in any neonate with microcephaly and epileptic encephalopathy.